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Online【GIR Open Seminar】 Dr. David Kisailus / University of California Irvine (U.S.A.), Dr. Yasuo Yoshikuni / Lawrence Berkeley National Laboratory (U.S.A.)

Date 2022.1.13 (9:00 - 11:00)
Venue Zoom
Speaker / Topic Google classroom is now available.
1. Go to https://classroom.google.com and sign in.
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※On-line Seminar by Zoom and then video streaming through Google Classroom later.
Meeting ID: 833 9718 1887
Pass Code: 408010

◆Dr. Yasuo Yoshikuni (Group Leader, US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, U.S.A)
〈Title: CRAGE enables rapid development of synthetic biology 〉

We developed chassis-independent recombinase-assisted genome engineering (CRAGE) and then extended its utility by developing CRAGE-duet. These CRAGE technologies enable single-step integration of large, complex DNA constructs directly into the chromosomes of diverse bacterial species across multiple phyla. Powerful applications are myriad. For example, CRAGE allows pathway engineering at the chromosome level and accelerates the DBTL cycle for industrial strain development. For instance, we developed a strain that can efficiently convert marine biomass to biofuels. The CRAGE systems also allow expression of single constructs in diverse chassis strains and testing of compatibility with the host's pathway. This multi-chassis approach enabled identification of ideal hosts for secondary metabolite biosynthesis and even allowed discovery of novel metabolites. In addition, the CRAGE systems are fully compatible with CRISPR systems; this compatibility enabled genome editing in non-model strains and thereby study of gene and pathway function. As a final example, we have started to use CRAGE systems to engineer root-associated microbes. This has allowed us to begin to understand spatiotemporal behaviors of bacteria in the rhizosphere and to create PGPRs that can significantly increase biomass yields. We believe that the speed, accuracy, efficiency, and versatility of CRAGE and CRAGE-Duet make them game-changing technologies in synthetic biology.

◆Dr. David Kisailus (Professor, Department of Materials Science and Engineering, University of California Irvine, U.S.A.)
〈Title: Biological Adaptations to Extreme Environments 〉

Over hundreds of millions of years, organisms have derived specific sets of traits in response to common selection pressures that serve as guideposts for optimal biological designs. A prime example is the evolution of toughened structures in disparate lineages within plants, invertebrates, and vertebrates. Extremely tough structures can function much like armor, battering rams, or reinforcements that enhance the ability of organisms to win competitions, find mates, acquire food, escape predation, and withstand high winds or turbulent flow. From an engineering perspective, biological solutions are intriguing because they must work in a multifunctional context. An organism rarely can be optimally designed for only one function or one environmental condition.
Some of these natural systems have developed well-orchestrated strategies, exemplified in the biological tissues of numerous animal and plant species, to synthesize and construct materials from a limited selection of available starting materials. The resulting structures display multiscale architectures with incredible fidelity and often exhibit properties that are similar, and frequently superior to, mechanical properties exhibited by many engineering materials. In specific instances, comparative analyses of multiscale structures have pinpointed which design principles have arisen convergently; when more than one evolutionary path arrives at the same solution, we have a good indication that it is the best solution. This is required for survival under extreme conditions. In this work, we describe a few of these systems that show convergent design and describe how controlled syntheses and hierarchical assembly using organic scaffolds lead to these integrated macroscale structures. We describe their function and its translation to biomimetic materials used for engineering applications.
Beyond this, we discuss a survival strategy of microbes that live in hyper-arid deserts. With high solar fluxes, including lethal UV radiation, severe shifts in temperature, high evaporation rate, and scarcity of water, these microorganisms, often the only biotic component of the ecosystem, find refuge inside rocks as a survival strategy. As such, these endolithic habitats provide a unique system to study processes at the biotic-abiotic interface under extreme environmental stresses. We show that the microorganisms can extract crystalline water from the rock under stressed conditions, subsequently inducing a phase transformation in the rock but enabling their survival. Results in this work not only shed light on how microorganisms can obtain water under severe xeric conditions, but also provide insights into potential life in even more extreme environments, such as Mars, as well as offer strategies for advanced water storage methods.

[1]. “Multiscale toughening mechanisms in biological materials and bioinspired designs,” W. Huang, D. Restrepo, J.Y. Jung, F.Y. Su, Z. Liu, R.O. Ritchie, J. McKittrick, P. Zavattieri, D. Kisailus, Advanced Materials, 31 (43) (2019) 1901561.
[2]. “Mechanism of water extraction from gypsum rock by desert colonizing microorganisms,” Wei Huang, Emine Ertekin, Taifeng Wang, Luz Cruz, Micah Daily, Jocelyne DiRuggiero, David Kisailus, PNAS, 117 (20) (2020) 10681-10687.
[3]. “Radular Stylus of Cryptochiton stelleri: A Multifunctional Lightweight and Flexible Fiber-Reinforced Composite,” Anna Pohl, Steven A. Herrera, David Restrepo, Ryo Negishi, Jae-Young Jung, Chris Salinas, Richard Wuhrer, Tomoko Yoshino, Joanna McKittrick, Atsushi Arakaki, Michiko Nemoto, Pablo Zavattieri, David Kisailus, Journal of the Mechanical Behavior of Biomedical Materials, 111 (2020) 103991.
[4]. “A natural impact resistant bi-continuous composite nanoparticle coating,” Wei Huang, Mehdi Shishehbor, Nicolás Guarín-Zapata, Nathan D. Kirchhofer, Jason Li, Luz Cruz, Taifeng Wang, Sanjit Bhowmick, Douglas Stauffer, Praveena Manimunda, Krassimir N. Bozhilov, Roy Caldwell, Pablo Zavattieri, David Kisailus, Nature Materials, 9 (11) (2020) 1236-1243.
[5]. “Toughening Mechanisms of the Elytra of the Diabolical Ironclad Beetle,” J. Rivera, M.S. Hosseini, D. Restrepo, S. Murata, D.Y. Parkinson, H.S. Barnard, A. Arakaki, P. Zavattieri, D. Kisailus, Nature, 586 (2020) 543-548.
[6]. “Modulation of impact energy dissipation in biomimetic helicoidal composites,” J. Rivera, N. Yaraghi, W. Huang, D. Gray, D. Kisailus, Journal of Materials Research and Technology, 9 (2020) 14619-14629.
[7]. “Structural Design Variations in Beetle Elytra”, Jesus Rivera, Satoshi Murata, Maryam Sadat Hosseini, Allison Pickle, Adwait A. Trikanad, Wen Yang, Nana Matsumoto, Dilworth Y. Parkinson, Harold S. Barnard, Pablo Zavattieri, Atsushi Arakaki, David Kisailus, Advanced Functional Materials, (2021) 2106468.
[8]. “Comparative proteomics reveals expression variations in major cuticular proteins of beetle elytra" Satoshi Murata, Jesus Rivera, Mi Yong Noh, Naoya Hiyoshi, Wen Yang, Dilworth Parkinson, Harold Barnard, Yasuyuki Arakane, David Kisailus, Atsushi Arakaki, Acta Biomaterialia, accepted (2021).
Language English
Intended for Everyone is welcome to join.
Co-Organized by Institute of Global Innovation Research, “ENERGY" Arakaki Team
Excellent Leader Development for Super Smart Society by New Industry Creation and Diversity
Contact Institute of Global Innovation Research, Institute of Engineering
Prof. Atsushi Arakaki
Email: arakakia(at)cc.tuat.ac.jp